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At least 991 records · Page 55Linked to original sources
PubMed2005

Butyrate suppresses tumor necrosis factor alpha production by regulating specific messenger RNA degradation mediated through a cis-acting AU-rich element.

OBJECTIVE: To study the capacity of butyrate to inhibit production of tumor necrosis factor alpha (TNFalpha) in macrophage-like synoviocytes (MLS) from patients with rheumatoid arthritis (RA), in human peripheral monocytes, and in murine RAW264.7 macrophages. METHODS: The concentrations of TNFalpha in culture supernatants of these cells were measured using enzyme-linked immunosorbent assay. The expression levels of various messenger RNAs (mRNA), such as those for TNFalpha, the mRNA-binding protein TIS11B, and luciferase, were measured using real-time quantitative polymerase chain reaction. The in vitro effects of butyrate on transcriptional regulation were evaluated by transfection with various reporter plasmids in RAW264.7 macrophages. The effects of TIS11B on TNFalpha expression were examined using an overexpression model of TIS11B in RAW264.7 cells. RESULTS: Butyrate suppressed TNFalpha protein and mRNA production in MLS and monocytes, but paradoxically enhanced transactivation of the TNFalpha promoter. Expression of the AU-rich element (ARE)-binding protein TIS11B was up-regulated by butyrate. Induction of TNFalpha mRNA by lipopolysaccharide was significantly inhibited when TIS11B was overexpressed. Butyrate facilitated the degradation of luciferase transcripts containing the 3'-untranslated region (3'-UTR) of TNFalpha, and this effect was dependent on the ARE in the 3'-UTR that is known to be involved in the regulation of mRNA degradation. CONCLUSION: These results indicate that butyrate suppresses TNFalpha expression by facilitating mRNA degradation mediated through a cis-acting ARE. Butyrate has the ability to regulate TNFalpha at the mRNA level and is therefore a potential therapeutic drug for RA patients.

3' Untranslated Regions↗
PubMed1992

Sodium vanadate, a tyrosine phosphatase inhibitor, affects expression of hematopoietic growth factors and extracellular matrix RNAs in SV40-transformed human marrow stromal cells.

Protein tyrosine kinases represent a subset of proteins that mediate signal transduction between the extracellular environment and the nucleus. We have previously described a coordinated upregulation between RNA transcripts of a tyrosine kinase, c-abl, and those of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin 6 (IL-6) in human marrow stromal cells (SVMSC). Moreover, an inverse relationship exists between expression of c-abl transcripts and those of extracellular matrix proteins such as type collagen I transcripts. In the present study, these inverse relationships were again seen in SVMSC when tyrosine kinase effects were enhanced by treatment of the cells with the tyrosine phosphatase inhibitor sodium orthovanadate. This suggests that tyrosine kinases are involved in the coordinate regulation of these genes.

Bone Marrow Cells↗
PubMed2026

Identifying Co-Expressed lncRNAs Correlated With Traits of Interest in an Animal Model for Metabolic Diseases in Humans.

Nutrigenomics investigates how nutrients modulate gene expression. Among them, fatty acids (FA) play important roles in regulating gene transcription, while long non-coding RNAs (lncRNAs) may be associated with gene regulation and metabolic diseases. This study aimed to analyze the hepatic transcriptome of pigs, a species frequently used as a model for nutrigenomic studies, to identify novel lncRNAs and their potential target genes in response to diets containing different sources of FA. Seventy-two pigs were fed four diets supplemented with 1.5% soybean oil (control), 3% canola oil, 3% fish oil, and 3% soybean oil. RNA sequencing of liver samples was performed to identify novel lncRNAs. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify modules associated with phenotypic traits related to lipid metabolism and inflammation. Functional enrichment analyses were then conducted to annotate genes within these modules using Gene Ontology (GO) terms and to assess overlap with Quantitative Trait Loci (QTL). The results revealed 106 novel lncRNAs potentially regulating genes associated with lipid metabolism and immune responses in pigs fed diets with different FA sources. These findings enhance understanding of the regulatory role of lncRNAs in pigs and reinforce their relevance as models for human metabolic diseases.

Animals↗
PubMed1991

Mitochondrial biogenesis in rabbit articular chondrocytes transferred to culture.

The effect of the switch to aerobic growth conditions was examined in rabbit articular chondrocytes transferred to culture. Spectroscopic analysis of the cytochromes of the respiratory chain shows that only cytochrome b is present in chondrocytes from cartilage, cytochromes c, c1, and a.a3 being undetectable as compared with the typical spectrum found in a primary cell culture on day 4. Steady state levels of RNA transcripts of nuclear (cytochrome c) and mitochondrial genes (cytochrome b and cytochrome oxidase subunits II and III) involved in the oxidative metabolism were determined relative to the RNA transcripts of the nuclear gene for glyceraldehyde phosphate dehydrogenase involved in the glycolytic pathway and to mitochondrial ribosomal RNAs. Chondrocytes transferred to culture showed a general increase in the levels of all transcripts, but the effect on mitochondrial transcripts was much greater (x 20) than the effect on nuclear transcripts (x 3-4). These results show the absence of a coordinate regulation of the expression of mitochondrial and nuclear genes coding for components of the respiratory chain. The increase in mitochondrial DNA triggered by culture conditions does not appear to be sufficient to account for the enhanced transcription. Concomitant with these mitochondrial changes, the level of transcripts for the collagen II gene involved in the differentiation function decreases dramatically (3% of the control on day 3).

Animals↗
PubMed2026

Phosphate backbone epitranscriptomics: Discovery of natural RNA phosphorothioates and their writer machinery.

Over 150 modifications expand the RNA alphabet, yet all known natural modifications occur on nucleobases or ribose sugars, with none identified on the phosphate backbone. In contrast, phosphorothioates (PSs), in which a non-bridging phosphate oxygen is replaced with sulfur, are central to RNA therapeutics but have never been reliably detected in natural RNAs. Here, we develop sequencing- and mass spectrometry-based approaches to quantitatively map RNA PSs at single-nucleotide resolution. Across diverse archaeal species, we identify stereospecific PS modifications at rRNA and tRNA hotspots, which are dynamically regulated by sulfur availability and temperature. We uncover a diverse enzyme family that selectively modifies tRNA/rRNA substrates and whose evolutionary presence/absence matches the distribution of PSs. Enzyme loss causes inviability or temperature sensitivity, and functional analyses reveal that tRNA PSs enhance tRNA stability. These findings establish the first natural RNA phosphate-backbone modification and its enzymatic machinery, providing a foundation for mechanistic and functional exploration.

RNA modifications↗
PubMed1996

Nerve growth factor induces the expression of certain cytokine genes and bcl-2 in mast cells. Potential role in survival promotion.

Nerve growth factor (NGF) promotes mast cell survival in vitro (Horigome, K., Bullock, E. D., and Johnson, E. M., Jr. (1994) J. Biol. Chem. 269, 2695-2702). NGF survival promotion is cell density-dependent, and conditioned medium experiments have shown that NGF increases the production of an autocrine mast cell survival activity. Cytokines are potential candidates for autocrine survival factors. In rat peritoneal mast cells (RPMC), NGF caused an increase in the messenger RNAs for interleukin (IL)-3, IL-4, IL-10, tumor necrosis factor-alpha, and granulocyte-macrophage colony-stimulating factor. This induction was NGF dose-dependent, was blocked by NGF-neutralizing antibodies, and was not observed in the non-mast peritoneal cell population. The immunosuppressive agent, cyclosporin A, blocked both cytokine induction and NGF-activated survival promotion but not survival promotion activated by IL-3 or stem cell factor, suggesting that NGF enhanced RPMC survival by increasing cytokine production. We also examine the effects of NGF on the expression levels of some members of the bcl-2 family and the interleukin-1beta-converting enzyme-like cysteine protease families. NGF markedly increased bcl-2 expression but had little or no effect on the other genes studied. The induction of bcl-2 mRNA by NGF was not blocked by cyclosporin A. These data suggest that induced cytokine gene expression but not increased expression of bcl-2 mediates NGF-survival promotion in RPMC.

Animals↗
PubMed2004

Roles of Brahma and Brahma/SWI2-related gene 1 in hypoxic induction of the erythropoietin gene.

Upon hypoxia, the human erythropoietin (EPO) gene is transactivated by the heterodimeric hypoxia-inducible factor 1 (HIF-1). Mammalian SWI/SNF is a chromatin-remodeling complex involved in the modulation of gene expression. We demonstrate that Brahma (Brm) and Brahma/SWI2-related gene 1 (Brg-1), alternative ATPase subunits of SWI/SNF, potentiate reporter gene activation mediated by HIF-1 in an ATPase-dependent manner. Brm was more potent than Brg-1 in the reporter gene assays. Simultaneous depletion of both Brm and Brg-1 by small interfering RNAs significantly compromised the transcription of the endogenous EPO gene triggered by hypoxia. Whereas knocking down Brm alone resulted in a moderate reduction in transcription of the EPO gene, depletion of Brg-1 resulted in an augmentation of transcription of both the EPO gene and the Brm gene, indicating that Brm can compensate for loss of Brg-1. Chromatin immunoprecipitation (ChIP) and sequential ChIP (re-ChIP) analysis showed that both Brm and Brg-1 associate with the enhancer region of the EPO gene in vivo in a hypoxia-dependent fashion and that each is present in a complex with HIF-1. Brm and Brg-1 were also recruited to the promoter of the vascular endothelial growth factor (VEGF) gene in a hypoxia-dependent fashion, although hypoxic induction of VEGF transcription was not affected by depletions of either or both Brm and Brg-1. Together these studies reveal a novel role for SWI/SNF in the activation of transcription of the EPO gene, indicate an important communication and compensation between Brm and Brg-1, and suggest that the requirement for SWI/SNF during hypoxic induction is gene-specific.

3' Untranslated Regions↗
PubMed2006

Knocking down type 2 but not type 1 calsequestrin reduces calcium sequestration and release in C2C12 skeletal muscle myotubes.

We examined the roles of type 1 and type 2 calsequestrins (CSQ1 and CSQ2) in stored Ca2+ release of C2C12 skeletal muscle myotubes. Transduction of C2C12 myoblasts with CSQ1 or CSQ2 small interfering RNAs effectively reduced the expression of targeted CSQ protein to near undetectable levels. As compared with control infected or CSQ1 knockdown myotubes, CSQ2 and CSQ1/CSQ2 knockdown myotubes had significantly reduced stored Ca2+ release evoked by activators of intracellular Ca2+ release channel/ryanodine receptor (10 mM caffeine, 200 microM 4-chloro-m-cresol, or 10 mM KCl). Thus, CSQ1 is not essential for effective stored Ca2+ release in C2C12 myotubes despite our in vitro studies suggesting that CSQ1 may enhance ryanodine receptor channel activity. To determine the basis of the reduced stored Ca2+ release in CSQ2 knockdown myotubes, we performed immunoblot analyses and found a significant reduction in both sarco/endoplasmic reticulum Ca2+-ATPase and skeletal muscle ryanodine receptor proteins in CSQ2 and CSQ1/CSQ2 knockdown myotubes. Moreover, these knockdown myotubes exhibited reduced Ca2+ uptake and reduced stored Ca2+ release by UTP (400 microM) that activates a different family of intracellular Ca2+ release channels (inositol 1,4,5-trisphosphate receptors). Taken together, our data suggest that knocking down CSQ2, but not CSQ1, leads to reduced Ca2+ storage and release in C2C12 myotubes.

Animals↗
PubMed2000

Rat protein kinase c zeta gene contains alternative promoters for generation of dual transcripts with 5'-end heterogeneity.

Protein kinase C (PKC) zeta is a phospholipid-dependent serine/threonine kinase that appears to perform important cell signaling functions. Two forms of PKC zeta RNA, with different 5' ends, have been reported. The major form (zeta) is expressed in most, if not all tissues, while the minor form (zeta'), which encodes the catalytic domain of the enzyme without most of its regulatory domain, is predominant in normal brain and certain rat prostate tumors. We report here the structure of the 5' end of the rat PKC zeta gene, demonstrating that both forms of RNA can be transcribed from the same gene through the use of alternative promoters and splicing. In luciferase reporter constructs, progressive deletions of the PKC zeta and zeta' 5' flanking sequences yielded activities that were higher in the cell lines expressing endogenous PKC zeta and zeta' RNAs, respectively. Also, multiple PCRs across different introns of the PKC zeta gene indicate that recent duplication of the gene or the existence of a closely related pseudogene in the rat genome are unlikely.

5' Untranslated Regions↗
PubMed1983

Sequential comparative hybridizations analyzed by computerized image processing can identify and quantitate regulated RNAs.

A method to analyze shifts in the relative abundance of many specific RNAs following any stimulus is presented. Hybridizations of two complex "total" cDNA probes (from the pre- and poststimulus states) to each member of a cDNA library are quantitatively analyzed and mathematically compared by using computer-assisted image processing and statistical analysis of sequential filter hybridizations. Experiments indicate that shifts in abundance between two states can be identified and reproducibly quantitated without purified probes. Direct isolation of recombinant cDNA colonies containing inserts corresponding to regulated RNAs is thus possible. The use of this system is demonstrated for partial analysis of the response in vivo of rat liver to glucocorticoids. Application to other biological systems in which a shift between two states occurs is discussed.

Animals↗
PubMed1994

Unusual in vivo turnover of transfer RNA in Vibrio cholerae.

Two lines of evidence suggest that, unlike in other organisms, the transfer RNAs of Vibrio cholerae undergo rapid turnover in vivo. Firstly, the tRNA content of V. cholerae cells treated with rifampicin (an inhibitor of initiation of RNA synthesis) decreased rapidly and continuously. Secondly, the newly synthesized tRNAs were rapidly degraded even under normal conditions of growth; the average half life of tRNA was 11.8 min. The degradation is mediated by an enzyme(s), present in V. cholerae cytoplasm, that apparently degrades tRNA completely. Rapid turnover is balanced by an enhanced rate of tRNA biogenesis, which was calculated to be 2.5 times higher than that in Escherichia coli.

Cell-Free System↗
PubMed2003

Hepatitis C virus RNA replication is resistant to tumour necrosis factor-alpha.

It was demonstrated using self-replicating hepatitis C virus (HCV) RNAs that both types of interferons (IFNs) (in particular IFN-alpha and IFN-gamma) are potent inhibitors of HCV replication in Huh-7 cells. Because IFN-gamma and tumour necrosis factor (TNF)-alpha trigger a partially overlapping set of antiviral defence mechanisms, it is tempting to speculate that TNF-alpha also inhibits HCV replication. However, this study shows that TNF-alpha does not affect HCV protein and RNA synthesis, nor does it synergistically enhance the inhibitory effect of IFN-gamma. Taken together, these results demonstrate that HCV replication in Huh-7 cells is highly resistant to TNF-alpha. It is, therefore, unlikely that the increased production of TNF-alpha, which is seen in many hepatitis C patients, contributes to HCV clearance by inducing antiviral defence mechanisms in infected hepatocytes.

Antiviral Agents↗
PubMed2005

The open reading frame VI product of Cauliflower mosaic virus is a nucleocytoplasmic protein: its N terminus mediates its nuclear export and formation of electron-dense viroplasms.

The Cauliflower mosaic virus (CaMV) open reading frame VI product (P6) is essential for the viral infection cycle. It controls translation reinitiation of the viral polycistronic RNAs and forms cytoplasmic inclusion bodies (viroplasms) where virus replication and assembly occur. In this study, the mechanism involved in viroplasm formation was investigated by in vitro and in vivo experiments. Far protein gel blot assays using a collection of P6 deletion mutants demonstrated that the N-terminal alpha-helix of P6 mediates interaction between P6 molecules. Transient expression in tobacco (Nicotiana tabacum) BY-2 cells of full-length P6 and P6 mutants fused to enhanced green fluorescent protein revealed that viroplasms are formed at the periphery of the nucleus and that the N-terminal domain of P6 is an important determinant in this process. Finally, this study led to the unexpected finding that P6 is a nucleocytoplasmic shuttle protein and that its nuclear export is mediated by a Leu-rich sequence that is part of the alpha-helix domain implicated in viroplasm formation. The discovery that P6 can localize to the nucleus opens new prospects for understanding yet unknown roles of this viral protein in the course of the CaMV infection cycle.

Active Transport, Cell Nucleus↗
PubMed2004

Adaptive mutations producing efficient replication of genotype 1a hepatitis C virus RNA in normal Huh7 cells.

Despite recent successes in generating subgenomic RNA replicons derived from genotype 1b strains of hepatitis C virus (HCV) that replicate efficiently in cultured cells, it has proven difficult to generate efficiently replicating RNAs from any other genotype of HCV. This includes genotype 1a, even though it is closely related to genotype 1b. We show here that an important restriction to replication of the genotype 1a H77c strain RNA in normal Huh7 cells resides within the amino-terminal 75 residues of the NS3 protease. We identified adaptive mutations located within this NS3 domain and within NS4A, in close proximity to the essential protease cofactor sequence, that act cooperative to substantially enhance the replication of this genotype 1a RNA in Huh7 cells. These and additional adaptive mutations, identified through a series of iterative transfections and the selection of G418-resistant cell clones, form two groups associating with distinct nonstructural protein domains: the NS3/4A protease and NS5A. A combination of mutations from both groups led to robust replication of otherwise unmodified H77c genomic RNA that was readily detectable by northern analysis within 4 days of transfection into Huh7 cells. We speculate that these adaptive mutations favorably influence assembly of the replicase complex with host cell-specific proteins, or alternatively promote interactions of NS3/4A and/or NS5A with cellular proteins involved in host cell antiviral defenses.

Cell Line↗
PubMed1984

In vitro transcription from the adenovirus 2 major late promoter utilizing templates truncated at promoter-proximal sites.

We report that adenovirus 2 DNA sequences located between positions-66 and -51 upstream of the major late cap site (position +1) enhance transcription initiation from this promoter by up to 5- to 10-fold in HeLa whole cell lysates. This enhancing effect is template concentration-dependent and is abolished by truncation of the template immediately upstream of -66. Additionally, specific transcripts are not detected from templates truncated at +33 downstream of the cap site. These results define a minimum region of approximately 100 base pairs encompassing the transcription start site that appears to interact with the RNA polymerase II transcription complex during initiation. Analysis of the shortest runoff transcripts that can be synthesized in vitro revealed that RNAs as short as 50 nucleotides are quantitatively modified by guanylylation and methylation to cap 1 structures. In contrast, short RNAs containing guanylylated but unmethylated cap structures are not efficiently utilized as substrates by endogenous cap-methylating enzymes in the HeLa lysate. These findings, together with the observation that the synthesis of short transcripts is sensitive to the presence of the methyltransferase inhibitor S-adenosylhomocysteine, suggest that cap formation is a promoter-proximal event that occurs concomitantly with the synthesis of a nascent RNA polymerase II transcript.

Adenoviruses, Human↗
PubMed1997

Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus.

The two ribozymes found in hepatitis delta virus RNA form related but non-identical secondary structures and display similar cleavage properties in vitro. Three of the non-duplex elements hypothesized to contribute nucleotides to the catalytic core vary slightly in length between the two ribozymes and the differences are conserved in clinical isolates. Possible functional relationships of the core sequence elements were tested by systematically exchanging sequences between the two ribozymes. It was found that switching two of the elements (L3 and J4/2) from one ribozyme to the other reduced cleavage activity in both. On the other hand, exchanging the third region (J1/4) resulted in enhanced activity for one ribozyme and a smaller increase in activity for the other. Combining exchanges did not reveal any compensatory interactions involving these particular elements nor did a pattern emerge that would suggest an optimal combination of core sequences for a generalized HDV ribozyme. Non-compensatory behavior reinforces the idea that the non-duplex sequences may form sequence-specific contacts with duplex portions of the ribozyme, but, in addition, these data suggest that there may be selective pressures on the ribozyme sequences in the virus that are not reflected in the in vitro self-cleavage assays.

Base Sequence↗
PubMed1991

Enhanced casein kinase II activity in COS-1 cells upon overexpression of either its catalytic or noncatalytic subunit.

Casein kinase II consists of catalytic (alpha) and regulatory (beta) subunits complexed into a heterotetrameric alpha 2 beta 2 structure. Full-length cDNAs encoding the alpha and beta subunits of human casein kinase II were subcloned into an expression vector containing the cytomegalovirus promotor, yielding the expression constructs pCMV-alpha and pCMV-beta. Northern analyses of total cellular RNA prepared from COS-1 fibroblasts 65 h after transfection with pCMV-alpha or pCMV-beta or with both expression constructs showed marked specific increases in corresponding alpha and beta subunit RNAs. Immunoblot analysis utilizing anti-casein kinase II antiserum of cytosolic extracts prepared from COS-1 cells co-transfected with pCMV-alpha and pCMV-beta showed 2- and 4-fold increases in immunoreactive alpha and beta subunit protein, respectively, relative to vector-transfected cells. These same cytosolic fractions exhibited an average 5-fold increase in casein kinase II catalytic activity. COS-1 cells transfected with pCMV-alpha alone exhibited a 3-fold increase in immunoreactive alpha subunit protein and a nearly 2-fold increase in cytosolic casein kinase II catalytic activity. Transfection with the cDNA coding for the noncatalytic beta subunit alone also caused a near doubling of cytosolic casein kinase II catalytic activity. No increase in immunoreactive alpha subunit protein was observed in pCMV-beta-transfected cells, and no increase in immunoreactive beta subunit protein was observed in pCMV-alpha-transfected cells. These results indicate that a portion of the endogenous cellular casein kinase II protein is not fully active and that raising the concentration of the alpha or beta subunit stimulates this latent activity.

Amino Acid Sequence↗
PubMed1980

The effects of tetraalkylammonium salts on helix-coil transition parameters in natural and synthetic ribo- and deoxyribo-polynucleotides.

Thermal transition profiles were recorded for a variety of natural and synthetic DNA and double-stranded RNA preparations in the presence of tetramethylammonium (TMA+) and tetraethylammonium (TEA+) cations. Double-stranded RNAs of natural origin, with GC contents of 50% exhibited the same profiles and Tm values as native DNA containing normal bases. Hence the tetraalkylammonium cations liquidate not only the effects of base composition, and the difference in stability between A-T and A-U base pairs (further confirmed by measurements with uracil-containing DNA from phage PBS-2), but also that of the 2'OH. In the presence of TMA+ cations, there is very marked enhancement of the stability of U-U base pairs in poly(rU) and poly(Um). In 2.4 M TEA, the 1:1 complex of poly(G) with poly (C) formed readily and melted reversibly with a Tm as low as 87 degrees C. At concentrations of TMA and TEA for which dTm/dXGC = 0, the Tm values for various phage DNA preparations containing atypical bases (phages T2, T4, phi e, phi W-14, PBS-2) differ appreciably from those with 'normal bases'. Analysis of these findings indicates that the selective interaction of TMA and TEA cations with A-T base pairs occurs in the minor groove of the DNA helix. The overall results show that the action of these quaternary ammonium cations is not due exclusively to preferential binding to A-T base pairs, but must involve other factors, including modifications of solvent structure. They also underline the utility of TMA and TEA solvent systems for placing in evidence transition profiles not accessible in other solvent systems.

DNA↗